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Opened 6 years ago
Closed 6 years ago
#2169 closed defect (duplicate)
Side View: self.view is None
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-4.4.0-154-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.91 (2019-06-29) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-06-29) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /data/disk3/modeling/gp14/gp14-refine.mrc Opened gp14-refine.mrc, grid size 400,400,400, pixel 1.05, shown at level -0.00314, step 2, values float32 > surface dust #1 size 40 > set bgColor black > set bgColor white > rainbow selAtoms > rainbow selAtoms > lighting full > lighting flat > lighting shadows true intensity 0.5 > set silhouettes false > set silhouettes true > view cofr false > open /data/disk3/modeling/gp14/MapToModel_1/map_to_model.pdb Summary of feedback from opening /data/disk3/modeling/gp14/MapToModel_1/map_to_model.pdb --- warnings | Ignored bad PDB record found on line 1 Ignored bad PDB record found on line 2 REMARK MODEL FROM PHENIX.MAP_TO_MODEL Ignored bad PDB record found on line 3 REMARK MAP FILE: /data/disk1/modeling/gp14/gp14-subunit-1.mrc Ignored bad PDB record found on line 4 Ignored bad PDB record found on line 610 Chain information for map_to_model.pdb #2 --- Chain | Description A | No description available > view cofr false > lighting full > lighting simple > lighting shadows true > lighting flat > lighting full > hide selAtoms surfaces > close #2 > volume selMaps style surface > vop gaussian #1 sdev 3.15 > volume selMaps projectionMode 2d-xyz > volume selMaps projectionMode 2d-xyz > hide #!2 models > close #2 > lighting full > lighting soft > lighting soft > lighting full > set bgColor gray > lighting soft > lighting flat > lighting shadows true intensity 0.5 > set silhouettes false > set silhouettes true > lighting full > lighting simple > lighting simple > lighting soft > set bgColor white > open /data/disk3/modeling/gp14-masked-flip-zone.mrc Opened gp14-masked-flip-zone.mrc, grid size 400,400,400, pixel 1.05, shown at level -6.1e-06, step 2, values float32 > hide #!1 models > view cofr false > lighting simple > lighting soft > lighting full > set bgColor white > set bgColor gray > surface dust #2 size 40 > lighting soft > lighting full > lighting full > lighting flat > lighting shadows true intensity 0.5 > set silhouettes false > view cofr false > set bgColor white > lighting simple > lighting soft > lighting full > lighting soft > lighting full > lighting soft > lighting soft > lighting soft > set bgColor white > set bgColor black > set bgColor gray > set bgColor white > set bgColor gray > lighting soft > lighting soft > lighting full > lighting soft > lighting simple > lighting simple > lighting soft > surface dust #2 size 40 > surface dust #2 size 40 > surface dust #2 size 80 > set bgColor white > help help:user > smoothlines #2 stepFactor 0.5 iterations 3 Surface model surface does not consist of lines > open /data/disk3/modeling/gp14/11-gp14-12.mrc Opened 11-gp14-12.mrc, grid size 400,400,400, pixel 1.05, shown at level 1.35e-07, step 2, values float32 > surface dust #1 size 40 > save session /data/disk3/modeling/gp14/11-gp14.cxs > open /data/disk3/modeling/gp14/11-gp14-12.mrc /data/disk3/modeling/gp14/11-gp14-12.pdb Summary of feedback from opening files --- warnings | Ignored bad PDB record found on line 94 REMARK MODEL FROM PHENIX.MAP_TO_MODEL Ignored bad PDB record found on line 95 REMARK MAP FILE: /data/disk1/modeling/gp14/gp14-subunit-1.mrc Ignored bad PDB record found on line 100 Ignored bad PDB record found on line 101 Opened 11-gp14-12.mrc, grid size 400,400,400, pixel 1.05, shown at level 1.35e-07, step 2, values float32 Chain information for 11-gp14-12.pdb --- Chain | Description 2.2/A | No description available > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > open /data/disk3/modeling/gp14/11-gp14-12.pdb Summary of feedback from opening /data/disk3/modeling/gp14/11-gp14-12.pdb --- warnings | Ignored bad PDB record found on line 94 REMARK MODEL FROM PHENIX.MAP_TO_MODEL Ignored bad PDB record found on line 95 REMARK MAP FILE: /data/disk1/modeling/gp14/gp14-subunit-1.mrc Ignored bad PDB record found on line 100 Ignored bad PDB record found on line 101 Chain information for 11-gp14-12.pdb #3 --- Chain | Description A | No description available > hide #!2.2 models > hide #!2 models > hide #!1 models > hide #!3 models > show #!3 models > open /data/disk3/modeling/gp14/11-gp14-12.pdb Chain information for 11-gp14-12.pdb #4 --- Chain | Description A B C D E F G H I J K L | No description available > nucleotides selAtoms tube/slab shape box > nucleotides selAtoms slab > style nucleic & selAtoms stick Changed 0 atom styles > volume selMaps show > style selAtoms ball Changed 6944 atom styles > style selAtoms sphere Changed 6944 atom styles > style selAtoms stick Changed 6944 atom styles > rainbow selAtoms > color selAtoms bychain Alignment identifier is 1 2 headers > interfaces selAtoms & ~solvent 19 buried areas: #2.2/A #4/L 3237, #3/A #4/L 3237, #2.2/A #3/A 3237, #2.2/A #4/A 918, #4/A #4/L 918, #3/A #4/A 918, #4/B #4/C 918, #4/D #4/E 918, #4/F #4/G 918, #4/F #4/E 918, #4/K #4/L 918, #3/A #4/K 918, #2.2/A #4/K 918, #4/I #4/J 918, #4/H #4/I 918, #4/D #4/C 918, #4/G #4/H 918, #4/A #4/B 918, #4/J #4/K 918 Attribute Qt::AA_EnableHighDpiScaling must be set before QCoreApplication is created. Attribute Qt::AA_EnableHighDpiScaling must be set before QCoreApplication is created. /usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/networkx/drawing/nx_pylab.py:579: MatplotlibDeprecationWarning: The iterable function was deprecated in Matplotlib 3.1 and will be removed in 3.3. Use np.iterable instead. if not cb.iterable(width): > show selAtoms ribbons > hide selAtoms > show selAtoms ribbons > hide selAtoms ribbons > show selAtoms surfaces > hide #!1 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!4 models > show #!4 models > show selAtoms ribbons > hide selAtoms surfaces > show #!3 models > show #!2.2 models > show #!1 models > hide #!1 models > show #!1 models > help help:user > hide #!1 models > show #!1 models > hide #!2.2 models > show #!2.2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!2 models > hide #!2.2 models > hide #!3 models > hide #!4 models > show #!4 models > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > hide #!4 models > hide #!3 models > show #!3 models > show #!2.2 models > close #2.2 > hide #!2 models > show #!2 models > show #!1 models > close #2 > show #!4 models > hide #!3 models > hide #!4 models > open /data/disk3/modeling/gp7.3-wt/gp7.3-norm.mrc /data/disk3/modeling/gp7.3-wt/wt-norm.mrc Opened gp7.3-norm.mrc, grid size 400,400,400, pixel 1.05, shown at level 0.0187, step 2, values float32 > view cofr false > hide #!2 models > show #!2 models > hide #!2.1 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.1 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > fitmap #2.1 inMap #2.2 Fit map gp7.3-norm.mrc in map wt-norm.mrc using 1142032 points correlation = 0.4602, correlation about mean = 0.09643, overlap = 25.81 steps = 132, shift = 0.848, angle = 2.33 degrees Position of gp7.3-norm.mrc (#2.1) relative to wt-norm.mrc (#2.2) coordinates: Matrix rotation and translation 0.99916988 0.04073759 0.00000494 0.00101946 -0.04073759 0.99916988 0.00000430 0.00151391 -0.00000476 -0.00000450 1.00000000 -0.84815058 Axis -0.00010800 0.00011911 -0.99999999 Axis point 0.03522359 -0.02655590 0.00000000 Rotation angle (degrees) 2.33473790 Shift along axis 0.84815064 > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > toolshed show "Side View" > hide #!2.1 models > show #!2.1 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > show #!3 models > hide #!3 models > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.1 models > show #!2.1 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 116, in exposeEvent self.render() File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) AttributeError: 'NoneType' object has no attribute 'use_shared_context' AttributeError: 'NoneType' object has no attribute 'use_shared_context' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) See log for complete Python traceback. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 116, in exposeEvent self.render() File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) AttributeError: 'NoneType' object has no attribute 'use_shared_context' AttributeError: 'NoneType' object has no attribute 'use_shared_context' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 384.130 OpenGL renderer: Quadro K2200/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → General Controls |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Side View: self.view is None |
comment:2 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #2162